I am running to issue using teiid, TEIID40095 TEIID31071 Invalid table; Table SugarCRMDataSourceJNDI_public.accounts_bugs_pkey has no columns defined. Is it a way to skip table with has no columns defined, instead of throwing exception?

There is not much information to go on. The error is saying that whatever data source you are pointing with the JNDI, the metadata creation at the deployment time is defining a table with no columns in it.

translator? resource adapter? version? how you are defining the VDB? is there any data in your source to create the models in the Teiid. What other debugging have you done to make sure sure that the error is with the Teiid? I already mentioned what is the error that Teiid is seeing, that needs to be rectified.